How can I update a specific layer of a multilayer exr file?
You do need to render out a new OpenEXR file.

Bring the OpenEXR files you already rendered into the compositor using an image sequence node. Then add a file output node and set it to OpenEXR multilayer. Reroute the outputs to combine the images as needed and re-render the sequence.



The basic procedure to setup the OpenEXR layers is outlined on this post:Combining .exr files?



You might need to render out a set of dummy files to automate the rendering.
See this post:Export multi-pass .exr image sequence from cycles?